This paper deals with protecting all-optical networks (AON) from security attacks at the physical level. It firstly presents an overall high level protocol for establishment, management and on-the-fly restoration of optimal secure lightpaths established by applying constraint-based open shortest path first (OSPF) source routing using proposed security databases of components. Secondly it presents a protocol for using fiber diversity between adjacent nodes to protect against attacks on fiber links. Thirdly it presents analytical models of propagation of security attacks on optical amplifiers and switches. These models are then used to develop security envelopes around these components, to calculate security indices and on-the-fly real-time restoration of components in case of an attack. Fourthly it presents simulation results for evaluation of the performance of these on-the-fly restoration schemes. These on-the-fly restoration schemes eliminate need for tearing down of attacked lightpaths and prevent consequent loss of large amount of data.